def test_format_database_command(self):
'''Test command to format database made correctly for blast+ and blastall'''
b_all_nuc = blast.Blast('ref.fasta', 'qry.fasta', blastall=True)
b_all_pro = blast.Blast('ref.fasta', 'qry.fasta', blast_type='blastp', blastall=True)
b_plus_nuc = blast.Blast('ref.fasta', 'qry.fasta')
b_plus_pro = blast.Blast('ref.fasta', 'qry.fasta', blast_type='blastp')
blastall_nuc = 'formatdb -p F -i ref.fasta'
blastall_pro = 'formatdb -p T -i ref.fasta'
blastplus_nuc = 'makeblastdb -dbtype nucl -in ref.fasta'
blastplus_pro = 'makeblastdb -dbtype prot -in ref.fasta'
self.assertEqual(b_all_nuc.format_database_command(), blastall_nuc)
self.assertEqual(b_all_pro.format_database_command(), blastall_pro)
self.assertEqual(b_plus_nuc.format_database_command(), blastplus_nuc)
self.assertEqual(b_plus_pro.format_database_command(), blastplus_pro)
query_file = 'tmp.test_blast_db_exists.fa'
b_blastn = blast.Blast(query_file, 'ref.fasta')
files = [query_file + '.' + x for x in ['nin', 'nhr', 'nsq']]
for f in files:
open(f, 'w').close()
self.assertEqual(b_blastn.format_database_command(), None)
for f in files:
os.unlink(f)
def test_make_options_string(self):
'''Test options set correctly'''
test_objs = [
blast.Blast('ref', 'qry'),
blast.Blast('ref', 'qry', evalue=0.1),
blast.Blast('ref', 'qry', word_size=42),
blast.Blast('ref', 'qry', no_filter=True),
blast.Blast('ref', 'qry', extra_options='-x 1'),
blast.Blast('ref', 'qry', blast_type='blastp'),
blast.Blast('ref', 'qry', blastall=True),
blast.Blast('ref', 'qry', blastall=True, evalue=0.1),
blast.Blast('ref', 'qry', blastall=True, word_size=42),
blast.Blast('ref', 'qry', blastall=True, no_filter=True),
]
correct = [
'-outfmt 6',
'-outfmt 6 -evalue 0.1',
'-outfmt 6 -word_size 42',
'-outfmt 6 -dust no',
'-outfmt 6 -x 1',
'-outfmt 6 -seg yes',
'-m 8',
'-m 8 -e 0.1',
'-m 8 -W 42',
'-m 8 -F F'
]
for i in range(len(correct)):
self.assertEqual(correct[i], test_objs[i]._make_options_string())
def test_make_io_string(self):
'''Test input/output files string'''
test_objs = [
blast.Blast('ref', 'qry'),
blast.Blast('ref', 'qry', blastall=True),
]
correct = [
'-db ref -query qry -out blast.out',
'-d ref -i qry -o blast.out',
]
for i in range(len(correct)):
self.assertEqual(correct[i], test_objs[i]._make_io_string())
def test_get_run_command(self):
'''Test command to run blast made OK'''
b = blast.Blast('qry.fasta', 'ref.fasta', evalue=0.1)
expected = ' '.join([
b._make_blast_type_string(),
b._make_io_string(),
b._make_options_string()
])
self.assertEqual(expected, b.get_run_command())
def test_blast_db_exists(self):
'''Test detection or not of blast database'''
query_file = 'tmp.test_blast_db_exists.fa'
b_blastn = blast.Blast(query_file, 'ref.fasta')
b_blastp = blast.Blast(query_file, 'ref.fasta', blast_type='blastp')
nuc_suffixes = ['nin', 'nhr', 'nsq']
nuc_suffixes2 = ['00.' + x for x in nuc_suffixes]
pro_suffixes = ['pin', 'phr', 'psq']
pro_suffixes2 = ['00.' + x for x in pro_suffixes]
open(query_file, 'w').close()
self.assertFalse(b_blastn.blast_db_exists())
self.assertFalse(b_blastp.blast_db_exists())
tuples = [
(nuc_suffixes, b_blastn, b_blastp),
(nuc_suffixes2, b_blastn, b_blastp),
(pro_suffixes, b_blastp, b_blastn),
(pro_suffixes2, b_blastp, b_blastn)
]
for suffixes, blast1, blast2 in tuples:
print((suffixes, blast1.blast_type, blast2.blast_type))
for suff in suffixes:
open(query_file + '.' + suff, 'w').close()
self.assertTrue(blast1.blast_db_exists())
self.assertFalse(blast2.blast_db_exists())
for suff in suffixes:
missing_file = query_file + '.' + suff
os.unlink(missing_file)
self.assertFalse(blast1.blast_db_exists())
open(missing_file, 'w').close()
for suff in suffixes:
os.unlink(query_file + '.' + suff)
os.unlink(query_file)
def __init__(self, options, farm_blast_script):
if options.outdir is None:
if options.blastall:
version = 'blastall'
else:
version = 'blast_plus'
options.outdir = '.'.join([
'Farm_blast',
os.path.basename(options.reference),
os.path.basename(options.query), version, options.blast_type,
'out'
])
self.outdir = os.path.abspath(options.outdir)
self.reference = os.path.abspath(options.reference)
self.query = os.path.abspath(options.query)
self.bsub_queue = options.bsub_queue
self.farm_blast_script = farm_blast_script
self.test = options.test
self.union_for_act = options.act
self.blast = blast.Blast(self.reference,
'query.split.INDEX',
outfile='tmp.array.out.INDEX',
blastall=options.blastall,
blast_type=options.blast_type,
evalue=options.evalue,
word_size=options.word_size,
no_filter=options.no_filter,
extra_options=options.blast_options)
self.setup_script = '01.setup.sh'
self.start_array_script = '02.run_array.sh'
self.combine_script = '03.combine.sh'
if options.bsub_name_prefix is None:
self.bsub_name_prefix = 'farm_blast:' + self.outdir
else:
self.bsub_name_prefix = options.bsub_name_prefix
if options.no_bsub:
self.no_bsub = True
self.memory_units = 'MB'
else:
self.no_bsub = False
self.memory_units = None
self.debug = options.debug
self.split_bases_tolerance = options.split_bases_tolerance
self.files_to_delete = [
'tmp.array.*',
'query.split.*',
'blast.out.tmp.gz',
'02.array.id',
'03.combine.sh.id',
]
if not options.blast_mem:
if self.blast.blastall and self.blast.blast_type == 'tblastx':
self.array_mem = 5
else:
self.array_mem = 0.5
if self.blast.no_filter:
self.array_mem *= 2
else:
self.array_mem = options.blast_mem
if not options.split_bases:
if self.blast.blastall and self.blast.blast_type == 'tblastx':
self.split_bases = 200000
else:
self.split_bases = 500000
else:
self.split_bases = options.split_bases
def test_make_blast_type_string(self):
'''Test blast type string'''
test_objs = [
(blast.Blast('ref', 'qry'), 'blastn -task blastn'),
(blast.Blast('ref', 'qry', blast_type='blastn'), 'blastn -task blastn'),
(blast.Blast('ref', 'qry', blast_type='blastn-short'), 'blastn -task blastn-short'),
(blast.Blast('ref', 'qry', blast_type='dc-megablast'), 'blastn -task dc-megablast'),
(blast.Blast('ref', 'qry', blast_type='megablast'), 'blastn -task megablast'),
(blast.Blast('ref', 'qry', blast_type='rmblastn'), 'blastn -task rmblastn'),
(blast.Blast('ref', 'qry', blast_type='blastx'), 'blastx'),
(blast.Blast('ref', 'qry', blast_type='blastp'), 'blastp -task blastp'),
(blast.Blast('ref', 'qry', blast_type='blastp-short'), 'blastp -task blastp-short'),
(blast.Blast('ref', 'qry', blast_type='deltablast'), 'blastp -task deltablast'),
(blast.Blast('ref', 'qry', blast_type='tblastn'), 'tblastn'),
(blast.Blast('ref', 'qry', blast_type='tblastx'), 'tblastx'),
(blast.Blast('ref', 'qry', blastall=True), 'blastall -p blastn'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='blastn'), 'blastall -p blastn'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='blastx'), 'blastall -p blastx'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='blastp'), 'blastall -p blastp'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='tblastn'), 'blastall -p tblastn'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='tblastx'), 'blastall -p tblastx'),
(blast.Blast('ref', 'qry', blastall=True, blast_type='megablast'), 'blastall -p blastn -n T')
]
for t in test_objs:
self.assertEqual(t[1], t[0]._make_blast_type_string())
with self.assertRaises(blast.Error):
b = blast.Blast('ref', 'qry', blast_type='oops')
def test_check_blast_type(self):
'''Check dies if blast_type not recognised'''
with self.assertRaises(blast.Error):
b = blast.Blast('query.fasta', 'ref.fasta', blast_type='oops')